Main Indicators
In order to partition networks into components or clusters, we deploy a community detection technique based on the Lovain Algorithm (Blondel et al., 2008). The Lovain Algorithm is a heuristic method that attempts to optimize the modularity of communities within a network by maximizing within- and minimizing between-community connectivity. We identify the following communities = knowledge bases.
| com | name | dgr_int | dgr |
|---|---|---|---|
| Knowledge Base 1: KB 1 | |||
| 1 | KOMANDER D. RAPE M. THE UBIQUITIN CODE (2012) | 7044 | 9075 |
| 1 | SWATEK K.N. KOMANDER D. UBIQUITIN MODIFICATIONS (2016) | 3968 | 4657 |
| 1 | YAU R. RAPE M. THE INCREASING COMPLEXITY OF THE UBIQUITIN CODE (2016) | 3669 | 4111 |
| 1 | HERSHKO A. CIECHANOVER A. THE UBIQUITIN SYSTEM (1998) | 3513 | 4543 |
| 1 | MEYER H.J. RAPE M. ENHANCED PROTEIN DEGRADATION BY BRANCHED UBIQUITIN CHAINS (2014) | 2729 | 2874 |
| 1 | HUSNJAK K. DIKIC I. UBIQUITIN-BINDING PROTEINS: DECODERS OF UBIQUITIN-MEDIATED CELLULAR FUNCTIONS (2012) | 2284 | 2755 |
| 1 | MEVISSEN T.E.T. KOMANDER D. MECHANISMS OF DEUBIQUITINASE SPECIFICITY AND REGULATION (2017) | 2213 | 2616 |
| 1 | YE Y. RAPE M. BUILDING UBIQUITIN CHAINS: E2 ENZYMES AT WORK (2009) | 1242 | 1327 |
| 1 | DESHAIES R.J. JOAZEIRO C.A. RING DOMAIN E3 UBIQUITIN LIGASES (2009) | 1167 | 1338 |
| 1 | XU P. DUONG D.M. SEYFRIED N.T. CHENG D. XIE Y. ROBERT J. RUSH J. PENG J. QUANTITATIVE PROTEOMICS REVEALS THE FUNCTION OF UNCONVENTIONAL UBIQUITIN C… | 1095 | 1130 |
| Knowledge Base 2: KB 2 | |||
| 2 | BRUGGNER R.V. BODENMILLER B. DILL D.L. TIBSHIRANI R.J. NOLAN G.P. AUTOMATED IDENTIFICATION OF STRATIFYING SIGNATURES IN CELLULAR SUBPOPULATIONS (2014) | 1498 | 1501 |
| 2 | VAN DER MAATEN L. HINTON G. VISUALIZING DATA USING T-SNE (2008) | 1159 | 1165 |
| 2 | WEBER L.M. ROBINSON M.D. COMPARISON OF CLUSTERING METHODS FOR HIGH-DIMENSIONAL SINGLE-CELL FLOW AND MASS CYTOMETRY DATA (2016) | 1093 | 1093 |
| 2 | SPITZER M.H. NOLAN G.P. MASS CYTOMETRY: SINGLE CELLS MANY FEATURES (2016) | 1036 | 1036 |
| 2 | LEVINE J.H. DATA-DRIVEN PHENOTYPIC DISSECTION OF AML REVEALS PROGENITOR-LIKE CELLS THAT CORRELATE WITH PROGNOSIS (2015) | 951 | 951 |
| 2 | SAMUSIK N. GOOD Z. SPITZER M.H. DAVIS K.L. NOLAN G.P. AUTOMATED MAPPING OF PHENOTYPE SPACE WITH SINGLE-CELL DATA (2016) | 889 | 893 |
| 2 | BENDALL S.C. NOLAN G.P. ROEDERER M. CHATTOPADHYAY P.K. A DEEP PROFILER’S GUIDE TO CYTOMETRY (2012) | 766 | 766 |
| 2 | BANDURA D.R. BARANOV V.I. ORNATSKY O.I. ANTONOV A. KINACH R. LOU X. PAVLOV S. TANNER S.D. MASS CYTOMETRY: TECHNIQUE FOR REAL TIME SINGLE CELL MULTI… | 748 | 748 |
| 2 | SHEKHAR K. BRODIN P. DAVIS M.M. CHAKRABORTY A.K. AUTOMATIC CLASSIFICATION OF CELLULAR EXPRESSION BY NONLINEAR STOCHASTIC EMBEDDING (ACCENSE) | 703 | 703 |
| 2 | KOTECHA N. KRUTZIK P.O. IRISH J.M. WEB-BASED ANALYSIS AND PUBLICATION OF FLOW CYTOMETRY EXPERIMENTS (2010) | 680 | 683 |
| Knowledge Base 3: KB 3 | |||
| 3 | MICHEAU O. TSCHOPP J. INDUCTION OF TNF RECEPTOR I-MEDIATED APOPTOSIS VIA TWO SEQUENTIAL SIGNALING COMPLEXES (2003) | 1658 | 3414 |
| 3 | HAAS T.L. EMMERICH C.H. GERLACH B. SCHMUKLE A.C. CORDIER S.M. RIESER E. FELTHAM R. WENGER T. RECRUITMENT OF THE LINEAR UBIQUITIN CHAIN ASSEMBLY COM… | 1224 | 1379 |
| 3 | KIRISAKO T. KAMEI K. MURATA S. KATO M. FUKUMOTO H. KANIE M. SANO S. IWAI K. A UBIQUITIN LIGASE COMPLEX ASSEMBLES LINEAR POLYUBIQUITIN CHAINS (2006) | 1211 | 1713 |
| 3 | DRABER P. KUPKA S. REICHERT M. DRABEROVA H. LAFONT E. DE MIGUEL D. SPILGIES L. HARTWIG T. LUBAC-RECRUITED CYLD AND A20 REGULATE GENE ACTIVATION AND… | 1034 | 1123 |
| 3 | GERLACH B. CORDIER S.M. SCHMUKLE A.C. EMMERICH C.H. RIESER E. HAAS T.L. WEBB A.I. WONG W.W. LINEAR UBIQUITINATION PREVENTS INFLAMMATION AND REGULAT… | 973 | 1079 |
| 3 | HE S. WANG L. MIAO L. WANG T. DU F. ZHAO L. WANG X. RECEPTOR INTERACTING PROTEIN KINASE-3 DETERMINES CELLULAR NECROTIC RESPONSE TO TNF-ALPHA (2009) | 959 | 989 |
| 3 | BERTRAND M.J. MILUTINOVIC S. DICKSON K.M. HO W.C. BOUDREAULT A. DURKIN J. GILLARD J.W. BARKER P.A. CIAP1 AND CIAP2 FACILITATE CANCER CELL SURVIVAL … | 958 | 999 |
| 3 | WANG L. DU F. WANG X. TNF-ALPHA INDUCES TWO DISTINCT CASPASE-8 ACTIVATION PATHWAYS (2008) | 871 | 1500 |
| 3 | OBERST A. DILLON C.P. WEINLICH R. MCCORMICK L.L. FITZGERALD P. POP C. HAKEM R. GREEN D.R. CATALYTIC ACTIVITY OF THE CASPASE-8-FLIP(L) | 811 | 834 |
| 3 | PELTZER N. RIESER E. TARABORRELLI L. DRABER P. DARDING M. PERNAUTE B. SHIMIZU Y. MONTINARO A. HOIP DEFICIENCY CAUSES EMBRYONIC LETHALITY BY ABERRAN… | 742 | 779 |
| Knowledge Base 4: KB 4 | |||
| 4 | MIETTINEN M. LASOTA J. GASTROINTESTINAL STROMAL TUMORS: PATHOLOGY AND PROGNOSIS AT DIFFERENT SITES (2006) | 1351 | 1351 |
| 4 | HIROTA S. ISOZAKI K. MORIYAMA Y. GAIN-OF-FUNCTION MUTATIONS OF C-KIT IN HUMAN GASTROINTESTINAL STROMAL TUMORS (1998) | 1285 | 1285 |
| 4 | VERWEIJ J. CASALI P.G. ZALCBERG J. PROGRESSION-FREE SURVIVAL IN GASTROINTESTINAL STROMAL TUMOURS WITH HIGH-DOSE IMATINIB: RANDOMISED TRIAL (2004) | 1116 | 1116 |
| 4 | HEINRICH M.C. CORLESS C.L. DUENSING A. PDGFRA ACTIVATING MUTATIONS IN GASTROINTESTINAL STROMAL TUMORS (2003) | 1070 | 1070 |
| 4 | DEMETRI G.D. VON MEHREN M. BLANKE C.D. EFFICACY AND SAFETY OF IMATINIB MESYLATE IN ADVANCED GASTROINTESTINAL STROMAL TUMORS (2002) | 1053 | 1053 |
| 4 | DEMETRI G.D. VAN OOSTEROM A.T. GARRETT C.R. EFFICACY AND SAFETY OF SUNITINIB IN PATIENTS WITH ADVANCED GASTROINTESTINAL STROMAL TUMOUR AFTER FAILUR… | 907 | 907 |
| 4 | BLANKE C.D. RANKIN C. DEMETRI G.D. PHASE III RANDOMIZED INTERGROUP TRIAL ASSESSING IMATINIB MESYLATE AT TWO DOSE LEVELS IN PATIENTS WITH UNRESECTAB… | 806 | 806 |
| 4 | HEINRICH M.C. CORLESS C.L. DEMETRI G.D. KINASE MUTATIONS AND IMATINIB RESPONSE IN PATIENTS WITH METASTATIC GASTROINTESTINAL STROMAL TUMOR (2003) | 739 | 739 |
| 4 | JOENSUU H. RISK STRATIFICATION OF PATIENTS DIAGNOSED WITH GASTROINTESTINAL STROMAL TUMOR (2008) | 723 | 723 |
| 4 | HEINRICH M.C. MAKI R.G. CORLESS C.L. PRIMARY AND SECONDARY KINASE GENOTYPES CORRELATE WITH THE BIOLOGICAL AND CLINICAL ACTIVITY OF SUNITINIB IN IMA… | 721 | 721 |
| Knowledge Base 5: KB 5 | |||
| 5 | GERLACH B. CORDIER S.M. SCHMUKLE A.C. EMMERICH C.H. RIESER E. HAAS T.L. LINEAR UBIQUITINATION PREVENTS INFLAMMATION AND REGULATES IMMUNE SIGNALLING… | 1414 | 1727 |
| 5 | HAAS T.L. EMMERICH C.H. GERLACH B. SCHMUKLE A.C. CORDIER S.M. RIESER E. RECRUITMENT OF THE LINEAR UBIQUITIN CHAIN ASSEMBLY COMPLEX STABILIZES THE T… | 1110 | 1326 |
| 5 | BOISSON B. LAPLANTINE E. DOBBS K. COBAT A. TARANTINO N. HAZEN M. HUMAN HOIP AND LUBAC DEFICIENCY UNDERLIES AUTOINFLAMMATION IMMUNODEFICIENCY AMYLOP… | 931 | 1069 |
| 5 | DRABER P. KUPKA S. REICHERT M. DRABEROVA H. LAFONT E. DE MIGUEL D. LUBAC-RECRUITED CYLD AND A20 REGULATE GENE ACTIVATION AND CELL DEATH BY EXERTING… | 893 | 1062 |
| 5 | BOISSON B. LAPLANTINE E. PRANDO C. GILIANI S. ISRAELSSON E. XU Z. IMMUNODEFICIENCY AUTOINFLAMMATION AND AMYLOPECTINOSIS IN HUMANS WITH INHERITED HO… | 880 | 995 |
| 5 | DAMGAARD R.B. WALKER J.A. MARCO-CASANOVA P. MORGAN N.V. TITHERADGE H.L. ELLIOTT P.R. THE DEUBIQUITINASE OTULIN IS AN ESSENTIAL NEGATIVE REGULATOR O… | 846 | 991 |
| 5 | ELLIOTT P.R. LESKE D. HRDINKA M. BAGOLA K. FIIL B.K. MCLAUGHLIN S.H. SPATA2 LINKS CYLD TO LUBAC ACTIVATES CYLD AND CONTROLS LUBAC SIGNALING (2016) | 770 | 910 |
| 5 | KEUSEKOTTEN K. ELLIOTT P.R. GLOCKNER L. FIIL B.K. DAMGAARD R.B. KULATHU Y. OTULIN ANTAGONIZES LUBAC SIGNALING BY SPECIFICALLY HYDROLYZING MET1-LINK… | 694 | 961 |
| 5 | FIIL B.K. DAMGAARD R.B. WAGNER S.A. KEUSEKOTTEN K. FRITSCH M. BEKKER-JENSEN S. OTULIN RESTRICTS MET1-LINKED UBIQUITINATION TO CONTROL INNATE IMMUNE… | 683 | 811 |
| 5 | KUPKA S. DE MIGUEL D. DRABER P. MARTINO L. SURINOVA S. RITTINGER K. SPATA2-MEDIATED BINDING OF CYLD TO HOIP ENABLES CYLD RECRUITMENT TO SIGNALING C… | 682 | 820 |
| Knowledge Base 6: KB 6 | |||
| 6 | GERLACH B. LINEAR UBIQUITINATION PREVENTS INFLAMMATION AND REGULATES IMMUNE SIGNALLING (2011) | 1492 | 1741 |
| 6 | HAAS T.L. RECRUITMENT OF THE LINEAR UBIQUITIN CHAIN ASSEMBLY COMPLEX STABILIZES THE TNF-R1 SIGNALING COMPLEX AND IS REQUIRED FOR TNF-MEDIATED GENE … | 1213 | 1374 |
| 6 | DRABER P. LUBAC-RECRUITED CYLD AND A20 REGULATE GENE ACTIVATION AND CELL DEATH BY EXERTING OPPOSING EFFECTS ON LINEAR UBIQUITIN IN SIGNALING COMPLE… | 976 | 1075 |
| 6 | DILLON C.P. RIPK1 BLOCKS EARLY POSTNATAL LETHALITY MEDIATED BY CASPASE-8 AND RIPK3 (2014) | 879 | 914 |
| 6 | JACO I. MK2 PHOSPHORYLATES RIPK1 TO PREVENT TNF-INDUCED CELL DEATH (2017) | 837 | 902 |
| 6 | SUN L. MIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN MEDIATES NECROSIS SIGNALING DOWNSTREAM OF RIP3 KINASE (2012) | 820 | 876 |
| 6 | NEWTON K. RIPK3 DEFICIENCY OR CATALYTICALLY INACTIVE RIPK1 PROVIDES GREATER BENEFIT THAN MLKL DEFICIENCY IN MOUSE MODELS OF INFLAMMATION AND TISSUE… | 768 | 799 |
| 6 | PELTZER N. HOIP DEFICIENCY CAUSES EMBRYONIC LETHALITY BY ABERRANT TNFR1-MEDIATED ENDOTHELIAL CELL DEATH (2014) | 765 | 848 |
| 6 | BERGER S.B. CUTTING EDGE: RIP1 KINASE ACTIVITY IS DISPENSABLE FOR NORMAL DEVELOPMENT BUT IS A KEY REGULATOR OF INFLAMMATION IN SHARPIN-DEFICIENT MI… | 736 | 770 |
| 6 | DEGTEREV A. IDENTIFICATION OF RIP1 KINASE AS A SPECIFIC CELLULAR TARGET OF NECROSTATINS (2008) | 711 | 745 |
| Knowledge Base 7: KB 7 | |||
| 7 | CRAIG R. BEAVIS R.C. TANDEM: MATCHING PROTEINS WITH TANDEM MASS SPECTRA (2004) | 1276 | 1276 |
| 7 | COX J. MANN M. MAXQUANT ENABLES HIGH PEPTIDE IDENTIFICATION RATES INDIVIDUALIZED P.P.B.-RANGE MASS ACCURACIES AND PROTEOME-WIDE PROTEIN QUANTIFICAT… | 705 | 1017 |
| 7 | ENG J.K. MCCORMACK A.L. YATES J.R. AN APPROACH TO CORRELATE TANDEM MASS SPECTRAL DATA OF PEPTIDES WITH AMINO ACID SEQUENCES IN A PROTEIN DATABASE (… | 427 | 446 |
| 7 | ELIAS J.E. GYGI S.P. TARGET-DECOY SEARCH STRATEGY FOR INCREASED CONFIDENCE IN LARGE-SCALE PROTEIN IDENTIFICATIONS BY MASS SPECTROMETRY (2007) | 353 | 380 |
| 7 | BOWDEN P. BEAVIS R. MARSHALL J. TANDEM MASS SPECTROMETRY OF HUMAN TRYPTIC BLOOD PEPTIDES CALCULATED BY A STATISTICAL ALGORITHM AND CAPTURED BY A RE… | 312 | 312 |
| 7 | SCHWARTZ J.C. SENKO M.W. SYKA J.E. A TWO-DIMENSIONAL QUADRUPOLE ION TRAP MASS SPECTROMETER (2002) | 304 | 304 |
| 7 | ENG J.K. JAHAN T.A. HOOPMANN M.R. COMET: AN OPEN-SOURCE MS/MS SEQUENCE DATABASE SEARCH TOOL (2013) | 295 | 295 |
| 7 | BENJAMINI Y. HOCHBERG Y. CONTROLLING FALSE DISCOVERY RATE: A PRACTICAL APPROACH TO MULTIPLE TESTING (1995) | 295 | 295 |
| 7 | BOWDEN P. META SEQUENCE ANALYSIS OF HUMAN BLOOD PEPTIDES AND THEIR PARENT PROTEINS (2010) | 294 | 294 |
| 7 | BOWDEN P. QUANTITATIVE STATISTICAL ANALYSIS OF STANDARD AND HUMAN BLOOD PROTEINS FROM LIQUID CHROMATOGRAPHY ELECTROSPRAY IONIZATION AND TANDEM MASS… | 294 | 294 |